rmsd/ub (RMSD upper bound) very flexible, asymmetric molecules
So, for example, a highly symmetrical rigid ligand could be rotated relative to a reference
conformation such that the new conformation is exactly equivalent to the reference
conformation (think of a benzene ring flipped 180 degrees).
However, the internal numbering of atoms doesn't change during the docking run, so the rmsd/ub algorithm,
which matches identically labeled atoms (rather than similar or equivalent atoms) would
yield a significant rmsd, whereas the rmsd/lb algorithm would yield a more realistic rmsd of zero in this case.
